Ontology highlight
ABSTRACT:
PROVIDER: PRJNA613573 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
Project description:This SuperSeries is composed of the following subset Series: GSE34655: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - mRNA-seq GSE34656: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - small RNA-seq GSE34657: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - Bisulfite-seq Refer to individual Series
2011-12-22 | E-GEOD-34658 | biostudies-arrayexpress
Project description:Assessment of individual whole cell transcriptional variation among closely related bacterial ecotypes
2012-05-01 | GSE37672 | GEO
Project description:DNA methylation is a conserved epigenetic mark in plants and many animals. How parental alleles interact in progeny to influence the epigenome is poorly understood. We analyzed the DNA methylomes of Arabidopsis Col and C24 ecotypes, and their hybrid progeny. Hy- brids displayed nonadditive DNA methylation levels, termed meth- ylation interactions, throughout the genome. Approximately 2,500 methylation interactions occurred at regions where parental DNA methylation levels are similar, whereas almost 1,000 were at differ- entially methylated regions in parents. Methylation interactions were characterized by an abundance of 24-nt small interfering RNAs. Furthermore, dysfunction of the RNA-directed DNA methylation pathway abolished methylation interactions but did not affect the increased biomass observed in hybrid progeny. Methylation interac- tions correlated with altered genetic variation within the genome, suggesting that they may play a role in genome evolution. Whole genome bisulfite sequencing and small RNA sequencing of the wild type and nrpd1nrpe1 double mutant background of parent Col ,C24, the hybrid ColXC24 and C24XCol to explore the role of the RdDM pathway in DNA methylation interactions.
2016-06-15 | E-GEOD-72993 | biostudies-arrayexpress
Project description:In the present study, we sought genes that are involved in the variation of the enhancement of plant growth rate among the Arabidopsis thaliana ecotypes in elevated CO2 condition. We performed a combination analysis of a genome wide association study (GWAS), and a transcriptome study to seek the candidate genes. GWAS was performed using the growth analysis data obtained at Oguchi et al. and the whole genome data from 31 ecotypes. The transcriptome analysis was performed for 6 ecotypes that had contrasting CO2 responses in the growth rate. We analyzed not only annotated coding genes but also small coding genes (30–100 amino acids) identified by Hanada et al., most of which were shown to play roles in cell-to-cell signaling, because it has been shown that a number of small coding genes play significant roles in environmental responses. We also studied the effect of the altered expression of the candidate genes on the plant growth rate in elevated CO2 condition using over-expression (OX) transgenics and RNA interference (RNAi) transgenics. We show that transgenic plants of three genes had significantly higher growth rate under the elevated CO2 condition.
2021-10-16 | GSE185907 | GEO
Project description:Multiomics of faecal samples collected from individuals in families with multiple cases of type 1 diabetes mellitus (T1DM) over 3 or 4 months. Metagenomic and metatranscriptomic sequencing and metaproteomics were carried out, as well as whole human genome sequencing. Phenotypic data is available.
2017-10-19 | MSV000081630 | MassIVE
Project description:Root branching in response to changes in nitrogen status in the soil, is a dramatic example of the plant’s remarkable developmental plasticity. In recent work we investigated the genetic architecture of developmental plasticity, combining phenoclustering and genome-wide association studies in 96 Arabidopsis thaliana ecotypes with expression profiling in 7 ecotypes, to characterise natural variation in root architectural plasticity at the phenotypic, genetic, and transcriptional levels. This series contains the microarray expression data for 7 ecotypes that represent a range of root branching strategies. We used microarrays to detail the global programme of gene expression involved in the plants response to nitrogen in the root and identified distinct classes of up- and down-regulated genes in the seven different Arabidopsis ecotypes during this process.
2013-09-01 | GSE34130 | GEO
Project description:Root branching in response to changes in nitrogen status in the soil, is a dramatic example of the plant’s remarkable developmental plasticity. In recent work we investigated the genetic architecture of developmental plasticity, combining phenoclustering and genome-wide association studies in 96 Arabidopsis thaliana ecotypes with expression profiling in 7 ecotypes, to characterise natural variation in root architectural plasticity at the phenotypic, genetic, and transcriptional levels. This series contains the microarray expression data for 7 ecotypes that represent a range of root branching strategies. We used microarrays to detail the global programme of gene expression involved in the plants response to nitrogen in the root and identified distinct classes of up- and down-regulated genes in the seven different Arabidopsis ecotypes during this process. The whole experiment was carried out in triplicate with 42 chips in total (14 experiments). The nitrogen response in seven Arabidopsis thaliana ecotype (Col0, Kas2, NFA8, SQ8, TAMM27, Ts5, Var2-1) whole roots was assayed using Affymetrix microarrays. Seedlings were grown hydroponically in low nitrogen for 12 days, then 5mM KNO3 was used as a nitrogen treatment for 2 hours with 5mM KCl used as a control treatment for the same length of time. At the end of the treatment time roots were harvested and flash-frozen in liquid nitrogen for subsequent RNA extraction. For *Probe_Elements_Removed* file descriptions, please see the Sample records' "Data processing" annotations.
2013-09-01 | E-GEOD-34130 | biostudies-arrayexpress
Project description:A small, shed antler fragment of a reindeer from Sjælland, Denmark has been dated to the Mid-Holocene, ca., 4700 cal B.C. Reindeer was an important component of the Lateglacial fauna in Denmark, and the species survived for ca. 1400 years into the Holocene. However, we consider it highly unlikely that this species inhabited Denmark during the Mid-Holocene, when dense forests characterized the vegetation and summer temperatures were somewhat higher than at present. We suggest that the reindeer antler came to Sjælland from Norway or Sweden as a result of trade, perhaps involving flint.
2021-11-25 | PXD024143 | Pride